- changed status to resolved
blocks parameter in plotIndiv with block.spls
Issue #94
resolved
Hi, When you use plotIndiv with a block.spls output and you use the parameter blocks, the names associated with each block displayed are not the right.
see code below
data("breast.TCGA")
## this is the X data as a list of mRNA and miRNA; the Y data set is a single data set of proteins
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna)
# set up a full design where every block is connected
design = matrix(1, ncol = length(data), nrow = length(data),
dimnames = list(names(data), names(data)))
diag(design) = 0
design
# set number of component per data set
ncomp = c(2)
# set number of variables to select, per component and per data set (this is set arbitrarily)
list.keepX = list(mrna = rep(20, 2), mirna = rep(10,2))
list.keepY = c(rep(10, 2))
TCGA.block.spls = block.spls(X = data, Y = breast.TCGA$data.train$protein,
ncomp = ncomp, keepX = list.keepX, keepY = list.keepY, design = design)
TCGA.block.spls
# in plotindiv we color the samples per breast subtype group but the method is unsupervised!
plotIndiv(TCGA.block.spls)
plotIndiv(TCGA.block.spls, blocks = c(3,2,1))
Comments (2)
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Hi,
Thanks for your message. There was indeed something wrong with the code. This has now been fixed with commit 598b158. It will be available in the next release. Thanks!
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Merged FlorianR/package-mixomics/devel into devel Fix issue
#94→ <<cset ba616a78d22a>>